ba-lab / pdnet
PDNET: A fully open-source framework for deep learning protein real-valued distances
☆34Updated 3 years ago
Related projects ⓘ
Alternatives and complementary repositories for pdnet
- Code associated with "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning."☆71Updated 6 months ago
- An unofficial re-implementation of AntiBERTy, an antibody-specific protein language model, in PyTorch.☆22Updated 8 months ago
- ☆34Updated 3 years ago
- Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure☆49Updated 2 years ago
- De novo protein structure prediction using iteratively predicted structural constraints☆55Updated 2 years ago
- Fork of matteofigliuzzi/bmDCA repository for Boltzmann-machine Direct Coupling Analysis (bmDCA).☆34Updated 4 years ago
- ☆29Updated 4 years ago
- Enzyme datasets used to benchmark enzyme-substrate promiscuity models☆29Updated 3 years ago
- PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms.☆27Updated last year
- Paratope Prediction using Deep Learning☆59Updated last year
- Code associated with the paper 'Cracking the blackbox of deep sequence-based protein-protein interaction prediction'☆19Updated 10 months ago
- Learning with uncertainty for biological discovery and design☆33Updated last year
- Code and data to reproduce analyses in Biswas et al. (2020) "Low-N protein engineering with data-efficient deep learning".☆56Updated 3 years ago
- Graph-based community clustering approach to extract protein domains from a predicted aligned error matrix☆32Updated 2 years ago
- ☆18Updated 3 years ago
- A surface-based deep learning approach for the prediction of ligand binding sites on proteins☆38Updated last year
- GREMLIN - learn MRF/potts model from input multiple sequence alignment! Implementation now available in C++ and Tensorflow/Python!☆53Updated 2 years ago
- ☆15Updated last year
- Protein design and variant prediction using autoregressive generative models☆22Updated last year
- mGPfusion is a Gaussian process based method for predicting stability changes upon single and multiple mutations of proteins that comple…☆15Updated 6 years ago
- Embedding-based annotation transfer (EAT) uses Euclidean distance between vector representations (embeddings) of proteins to transfer ann…☆28Updated 2 years ago
- Code for our paper "Protein sequence design with a learned potential"☆77Updated last year
- The standalone version of SPOT-1D-Single available for public use for research purposes.☆23Updated 6 months ago
- Computational tools for extremely low-cost, massively parallel amplicon-based sequencing of every variant in protein mutant libraries.☆30Updated 2 years ago
- A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.☆38Updated last year
- Direct coupling analysis software for protein and RNA sequences☆47Updated last year
- Improved antibody structure-based design using inverse folding☆75Updated 2 months ago
- Nature Methods: RhoFold+, Accurate RNA 3D structure prediction using a language model-based deep learning approach☆42Updated 9 months ago
- Protein design and variant prediction using autoregressive generative models☆93Updated 10 months ago